The rule in Greece is, in high-season there’s the possibility that a ferry could sell out—but it’s not likely.
In September you should have no problem getting on the train or ferry that you need. Even if seats were to selI out, you can still get on board as a standing passenger. I usually buy ferry tix at the dock the day before departure—mostly to save time at the ticket window in the morning, but also to see where the boat departs from. If you have to catch a ferry that leaves around sunrise, it’s a good idea to check out the port or dock it leaves from so you’re able to recognize it before you’ve had the morning’s first cup of coffee.
Have fun in Greece!